# All Questions

5,182 questions
754 views

### How can I update a map/mesh and coordinates in a PyMol session file?

I have a PyMol session file I was using to create my figures. It contains a protein and ligand broken into several groups of atoms with a fair bit of overlap. There are also a few meshes built from ...
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### Synthesis Golf X: TAK-457

I shall try to revive this! A full FAQ post has been written on chemistry.meta.SE, explaining the premise of synthesis golf and the 'rules'. Please take a look at this before answering (if you haven't ...
194 views

### Single-molecule magnet with electrically-controlled permeability: How does the Titan Shield from Deus Ex work?

In a recent installment of Deus Ex game series there is an augmentation called "Titan Shield" (it has nothing to do with $\ce{Ti}$ element): A neodymium skin underlay matrix built of nano-meshed ...
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### Ambimodal transition states in some organic reaction pathways

In many computational studies, mechanisms appear to have so-called ambimodal transition states, i.e. a transition state which can lead to multiple products, in conflict to the common undergraduate ...
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### How does the cyclopropyl group influence conjugation and aromaticity?

While answering the question Why isn't cyclobutane planar?, I recollected that cyclopropane and its derivatives behave like double-bond compounds, e.g. a cyclopropyl group can potentially be ...
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### f-electrons in chemistry of heavy transition metals

In one lecture on recent MCR-X conference I was puzzled by a side-note "f-hole is critical to describe DoS of $\ce{IrO2}$ correctly." The context was DFT periodic plane-wave calculations with ...
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### Is there a consensus on whether amber can seal in air bubbles for millions of years?

I read about deriving the oxygen content in the atmosphere in the Cretaceous by analyzing the air trapped in bubbles in amber from that period, but I have also found papers disputing the study's ...
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### How to Calculate Transition Dipole Moment from Two Known Wavefunctions

I am interested in calculating the transition dipole moment (TDM) from the information from two wavefunctions of different states. This is somewhat similar to calculating the molecular dipole moment ...
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### Melting and boiling point trend in Group II

The following picture shows the melting and boiling point trends down group II elements. I have added question marks where the variability in data was rather disturbing (over two hundred degrees ...
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### Neighbouring group participation with and without retention of configuration in nucleophilic substitution of 2,6-dichloro-9-thiabicyclo[3.3.1]nonane

Treatment of the dichloride A under the conditions indicated gives B with retention of configuration, while treatment of dichloride C gives D with inversion of configuration. I am having ...
185 views

### Why does a Diels–Alder reaction not occur here?

I have recently come across this organic chemistry problem. I thought it would undergo simple Diels–Alder reaction But it didn't turn out to be. The product to me looks like a nucleophilic attack ...
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### Physical meaning of thermal parameters dimension (Å²)

In single-crystal x-ray crystallography both isotropic and anisotropic displacement parameters $U_{ij}$ of thermal ellipsoids have dimension of square angstrom ($Å^2$) as follows from the definition ...
132 views

### Accuracy of quantum chemistry calculations on iodine neglecting relativistic effects

Triiodothyronine is a molecule with three iodine atoms. If we attempted to calculate its properties with ab initio methods like Hartree-Fock or more complicated ab initio methods which included ...
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### Some materials emit more photoelectrons than others - why?

Again, I'm a physicist turning to chemists (so bear with me). So I've been measuring some materials by changing the wavelength of the incident light on the material and I have a detecting tip like in ...
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### Synthesis of Anthracene: Mechanism

Recently, I happened to find a problem that involved the synthesis of anthracene from bromobenzene in the presence of tert-butyl lithium, using THF as the solvent, and at room temperature. I am ...
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Shannon, R. D., 1976, Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides: Acta Crystallographica Section A, v. 32, p. 751–767. DOI: 10.1107/...
162 views

### Transition state optimisation on the surface of periclase

I want to model a reaction catalysed by periclase ($\ce{MgO}$) using DFT. I have a good guess on the transition state (TS) of the reaction that goes in gas phase/solvent (produced using MOPAC). The ...
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### How to color bonds by the strain?

I need to create a figure of a molecule in which the bonds are colored in a RGB scale according to the values read from a data file. The data file contains, for example, the increase or decrease in ...
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### What is the difference between Fukui FMO approach and Woodward-Hoffmann rules?

If I understand correctly Frontier MO-theory is based on the perturbation theory of reactivity and the Woodward-Hoffmann rules consider conservation of orbital symmetry. Does FMO use symmetry ...
537 views

### Mixing two containers of each water and ethanol to varying degrees of purity

In the following question, the water/wine mixing problem was recast in chemical terms. However, partial molar volumes can make this a much more challenging problem than it appears on the surface. ...